From: Visualizing genomic information across chromosomes with PhenoGram
Usage: pheno_gram.rb | Â |
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-h --help | Show the help message and exit |
-v --version | Show PhenoGram version |
-i input filename | Filename of input configuration file |
-o output filename | Filename of output plot |
-t title | Main plot title (enclose in double quotes) |
-f image type | Output image format (default is PNG); other options depend on ImageMagick installation |
-p phenotype spacing | Determines standard, equal, or alternative algorithm |
-c color range | Determines random, web, generator, group, or list algorithm |
-z --high-res | Sets plot resolution to 1200 DPI |
-C --chrom-only | Plot only chromosomes with position |
-S --small-circle | Plot with smaller phenotype circles |
-O --outline-circle | Plot phenotype circles with black outline |
-Z zoom location | Zoom on chromosome (i.e. 7) or region (i.e. 7:10000–20000) |
-a --include-annotation | Include annotation on plot |
-T --trans-lines | Show more transparent lines on chromosomes |
-n --thin-lines | Show thinner lines across chromosomes |
-B --thick-boundary | Increase thickness of chromosome boundary |
-F --big-font | Increase font size of phenotype labels |
-x –shade-chromatin | Add shading to inaccessible or cytogenetic chromosome regions |
-r random seed | Seed for random number generator (default is 7) |